Microbial Genome Sequencing: Algal Virus Genomics

University Of Massachusetts Lowell, Lowell MA

Investigators

Abstract

A grant has been awarded to Drs. Michael Graves of the University of Massachusetts (Lowell) and James Van Etten of the University of Nebraska (Lincoln) to sequence the genomes of 4 genetically diverse viruses that infect certain unicellular, eukaryotic, chlorella-like green algae found in freshwater environments worldwide. The chlorella virus genomes are very large; one isolate, PBCV-1, (genome size = 330,744 bp dsDNA) codes for 11 tRNAs and ~375 proteins, nearly half of which resemble proteins of known function. Many of these genes encode proteins (e.g. DNA restriction endonucleases and enzymes involved in protein glycosylation) rarely associated with viruses. Comparisons between PBCV-1 and other chlorella viruses indicate they are very diverse; the entire "gene pool" of the chlorella viruses exceeds the 375 PBCV-1-encoded genes. Therefore, the sequence of a single isolate does not give the total picture and many new genes await discovery among the numerous isolates. The sizes of the chlorella virus genomes (> 300 kbp) are comparable to bacterial artificial chromosomes (BACs) and therefore technologies developed for shotgun subcloning and sequencing BACs will be employed. Additionally, chlorella virus genomes contain little repetitive sequence and their genes are densely packed; therefore, every sequence read will contain at least part of a gene. At present, the study of algal viruses is in its infancy. Algae play an important role in aquatic environments and algal viruses play a significant, albeit poorly understood, role in regulating algal communities, e.g. destroying toxic algal blooms such as those responsible for red tides and brown tides. Therefore, the study of algal viruses is critical to a better understanding of the dynamics of aquatic environments. The knowledge gained from this study will help to advance the study of algal virology and the roles these viruses play in their environment. While the sequence of chlorella virus PBCV-1 led to an increase in our knowledge of the genome structure of large dsDNA algal viruses, it also revealed how little we know. Undoubtedly, the genomic sequences of additional chlorella viruses will identify new genes that encode proteins that are both scientifically interesting and may have commercial value. Finally, the information gained from this research will advance the study of the evolutionary history, not only of all algal viruses, but also the evolutionary histories of the other families of large dsDNA viruses such as the pox viruses and herpes viruses.